@article{coffer_graybill_whitman_schaeffer_salls_zimmerman_hill_lebrasse_li_keith_et al._2023, title={Providing a framework for seagrass mapping in United States coastal ecosystems using high spatial resolution satellite imagery}, volume={337}, ISSN={["1095-8630"]}, DOI={10.1016/j.jenvman.2023.117669}, abstractNote={Seagrasses have been widely recognized for their ecosystem services, but traditional seagrass monitoring approaches emphasizing ground and aerial observations are costly, time-consuming, and lack standardization across datasets. This study leveraged satellite imagery from Maxar's WorldView-2 and WorldView-3 high spatial resolution, commercial satellite platforms to provide a consistent classification approach for monitoring seagrass at eleven study areas across the continental United States, representing geographically, ecologically, and climatically diverse regions. A single satellite image was selected at each of the eleven study areas to correspond temporally to reference data representing seagrass coverage and was classified into four general classes: land, seagrass, no seagrass, and no data. Satellite-derived seagrass coverage was then compared to reference data using either balanced agreement, the Mann-Whitney U test, or the Kruskal-Wallis test, depending on the format of the reference data used for comparison. Balanced agreement ranged from 58% to 86%, with better agreement between reference- and satellite-indicated seagrass absence (specificity ranged from 88% to 100%) than between reference- and satellite-indicated seagrass presence (sensitivity ranged from 17% to 73%). Results of the Mann-Whitney U and Kruskal-Wallis tests demonstrated that satellite-indicated seagrass percentage cover had moderate to large correlations with reference-indicated seagrass percentage cover, indicative of moderate to strong agreement between datasets. Satellite classification performed best in areas of dense, continuous seagrass compared to areas of sparse, discontinuous seagrass and provided a suitable spatial representation of seagrass distribution within each study area. This study demonstrates that the same methods can be applied across scenes spanning varying seagrass bioregions, atmospheric conditions, and optical water types, which is a significant step toward developing a consistent, operational approach for mapping seagrass coverage at the national and global scales. Accompanying this manuscript are instructional videos describing the processing workflow, including data acquisition, data processing, and satellite image classification. These instructional videos may serve as a management tool to complement field- and aerial-based mapping efforts for monitoring seagrass ecosystems.}, journal={JOURNAL OF ENVIRONMENTAL MANAGEMENT}, author={Coffer, Megan M. and Graybill, David D. and Whitman, Peter J. and Schaeffer, Blake A. and Salls, Wilson B. and Zimmerman, Richard C. and Hill, Victoria and Lebrasse, Marie Cindy and Li, Jiang and Keith, Darryl J. and et al.}, year={2023}, month={Jul} }
 @article{whitman_schaeffer_salls_coffer_mishra_seegers_loftin_stumpf_werdell_2022, title={A validation of satellite derived cyanobacteria detections with state reported events and recreation advisories across US lakes}, volume={115}, ISSN={["1878-1470"]}, DOI={10.1016/j.hal.2022.102191}, abstractNote={Cyanobacteria harmful algal blooms (cyanoHABs) negatively affect ecological, human, and animal health. Traditional methods of validating satellite algorithms with data from water samples are often inhibited by the expense of quantifying cyanobacteria indicators in the field and the lack of public data. However, state recreation advisories and other recorded events of cyanoHAB occurrence reported by local authorities can serve as an independent and publicly available dataset for validation. State recreation advisories were defined as a period delimited by a start and end date where a warning was issued due to detections of cyanoHABs over a state's risk threshold. State reported events were defined as any event that was documented with a single date related to cyanoHABs. This study examined the presence-absence agreement between 160 state reported cyanoHAB advisories and 1,343 events and cyanobacteria biomass estimated by a satellite algorithm called the Cyanobacteria Index (CIcyano). The true positive rate of agreement with state recreation advisories was 69% and 60% with state reported events. CIcyano detected a reduction or absence in cyanobacteria after 76% of the recreation advisories ended. CIcyano was used to quantify the magnitude, spatial extent, and temporal frequency of cyanoHABs; each of these three metrics were greater (r > 0.2) during state recreation advisories compared to non-advisory times with effect sizes ranging from small to large. This is the first study to quantitatively evaluate satellite algorithm performance for detecting cyanoHABs with state reported events and advisories and supports informed management decisions with satellite technologies that complement traditional field observations.}, journal={HARMFUL ALGAE}, author={Whitman, Peter and Schaeffer, Blake and Salls, Wilson and Coffer, Megan and Mishra, Sachidananda and Seegers, Bridget and Loftin, Keith and Stumpf, Richard and Werdell, P. Jeremy}, year={2022}, month={Jun} }
 @article{lebrasse_schaeffer_zimmerman_hill_coffer_whitman_salls_graybill_osburn_2022, title={Simulated response of St. Joseph Bay, Florida, seagrass meadows and their belowground carbon to anthropogenic and climate impacts}, volume={179}, ISSN={["1879-0291"]}, DOI={10.1016/j.marenvres.2022.105694}, abstractNote={Seagrass meadows are degraded globally and continue to decline in areal extent due to human pressures and climate change. This study used the bio-optical model GrassLight to explore the impact of climate change and anthropogenic stressors on seagrass extent, leaf area index (LAI) and belowground organic carbon (BGC) in St. Joseph Bay, Florida, using water quality data and remotely-sensed sea surface temperature (SST) from 2002 to 2020. Model predictions were compared with satellite-derived measurements of seagrass extent and shoot density from the Landsat images for the same period. The GrassLight-derived area of potential seagrass habitat ranged from 36.2 km2 to 39.2 km2, averaging 38.0 ± 0.8 km2 compared to an observed seagrass extent of 23.0 ± 3.0 km2 derived from Landsat (range = 17.9–27.4 km2). GrassLight predicted a mean seagrass LAI of 2.7 m2 leaf m−2 seabed, compared to a mean LAI of 1.9 m2 m−2 estimated from Landsat, indicating that seagrass density in St. Joseph Bay may have been below its light-limited ecological potential. Climate and anthropogenic change simulations using GrassLight predicted the impact of changes in temperature, pH, chlorophyll a, chromophoric dissolved organic matter and turbidity on seagrass meadows. Simulations predicted a 2–8% decline in seagrass extent with rising temperatures that was offset by a 3–11% expansion in seagrass extent in response to ocean acidification when compared to present conditions. Simulations of water quality impacts showed that a doubling of turbidity would reduce seagrass extent by 18% and total leaf area by 21%. Combining climate and water quality scenarios showed that ocean acidification may increase seagrass productivity to offset the negative effects of both thermal stress and declining water quality on the seagrasses growing in St. Joseph Bay. This research highlights the importance of considering multiple limiting factors in understanding the effects of environmental change on seagrass ecosystems.}, journal={MARINE ENVIRONMENTAL RESEARCH}, author={Lebrasse, Marie Cindy and Schaeffer, Blake A. and Zimmerman, Richard C. and Hill, Victoria J. and Coffer, Megan M. and Whitman, Peter J. and Salls, Wilson B. and Graybill, David D. and Osburn, Christopher L.}, year={2022}, month={Jul} }
 @article{lebrasse_schaeffer_coffer_whitman_zimmerman_hill_islam_li_osburn_2022, title={Temporal Stability of Seagrass Extent, Leaf Area, and Carbon Storage in St. Joseph Bay, Florida: a Semi-automated Remote Sensing Analysis}, volume={3}, ISSN={["1559-2731"]}, DOI={10.1007/s12237-022-01050-4}, abstractNote={Abstract}, journal={ESTUARIES AND COASTS}, author={Lebrasse, Marie Cindy and Schaeffer, Blake A. and Coffer, Megan M. and Whitman, Peter J. and Zimmerman, Richard C. and Hill, Victoria J. and Islam, Kazi A. and Li, Jiang and Osburn, Christopher L.}, year={2022}, month={Mar} }
 @article{coffer_whitman_schaeffer_hill_zimmerman_salls_lebrasse_graybill_2022, title={Vertical artifacts in high-resolution WorldView-2 and WorldView-3 satellite imagery of aquatic systems}, volume={43}, ISSN={["1366-5901"]}, DOI={10.1080/01431161.2022.2030069}, abstractNote={ABSTRACT Satellite image artefacts are features that appear in an image but not in the original imaged object and can negatively impact the interpretation of satellite data. Vertical artefacts are linear features oriented in the along-track direction of an image system and can present as either banding or striping; banding are features with a consistent width, and striping are features with inconsistent widths. This study used high-resolution data from DigitalGlobeʻs (now Maxar) WorldView-3 satellite collected at Lake Okeechobee, Florida (FL), on 30 August 2017. This study investigated the impact of vertical artefacts on both at-sensor radiance and a spectral index for an aquatic target as WorldView-3 was primarily designed as a land sensor. At-sensor radiance measured by six of WorldView-3ʻs eight spectral bands exhibited banding, more specifically referred to as non-uniformity, at a width corresponding to the multispectral detector sub-arrays that comprise the WorldView-3 focal plane. At-sensor radiance measured by the remaining two spectral bands, red and near-infrared (NIR) #1, exhibited striping. Striping in these spectral bands can be attributed to their time delay integration (TDI) settings at the time of image acquisition, which were optimized for land. The impact of vertical striping on a spectral index leveraging the red, red edge, and NIR spectral bands—referred to here as the NIR maximum chlorophyll index (MCINIR)—was investigated. Temporally similar imagery from the European Space Agencyʻs Sentinel-3 and Sentinel-2 satellites were used as baseline references of expected chlorophyll values across Lake Okeechobee as neither Sentinel-3 nor Sentinel-2 imagery showed striping. Striping was highly prominent in the MCINIR product generated using WorldView-3 imagery, as noise in the at-sensor radiance exceeded any signal of chlorophyll in the image. Adjusting the image acquisition parameters for future tasking of WorldView-3 or the functionally similar WorldView-2 satellite may alleviate these artefacts. To test this, an additional WorldView-3 image was acquired at Lake Okeechobee, FL, on 26 May 2021 in which the TDI settings and scan line rate were adjusted to improve the signal-to-noise ratio. While some evidence of non-uniformity remained, striping was no longer noticeable in the MCINIR product. Future image tasking over aquatic targets should employ these updated image acquisition parameters. Since the red and NIR #1 spectral bands are critical for inland and coastal water applications, archived images not collected using these updated settings may be limited in their potential for analysis of aquatic variables that require these two spectral bands to derive.}, number={4}, journal={INTERNATIONAL JOURNAL OF REMOTE SENSING}, author={Coffer, Megan M. and Whitman, Peter J. and Schaeffer, Blake A. and Hill, Victoria and Zimmerman, Richard C. and Salls, Wilson B. and Lebrasse, Marie C. and Graybill, David D.}, year={2022}, month={Feb}, pages={1199–1225} }
 @article{wu_hilborn_schaeffer_urquhart_coffer_lin_egorov_2021, title={Acute health effects associated with satellite-determined cyanobacterial blooms in a drinking water source in Massachusetts}, volume={20}, ISSN={["1476-069X"]}, url={https://doi.org/10.1186/s12940-021-00755-6}, DOI={10.1186/s12940-021-00755-6}, abstractNote={Abstract}, number={1}, journal={ENVIRONMENTAL HEALTH}, author={Wu, Jianyong and Hilborn, Elizabeth D. and Schaeffer, Blake A. and Urquhart, Erin and Coffer, Megan M. and Lin, Cynthia J. and Egorov, Andrey I}, year={2021}, month={Jul} }
 @article{coffer_schaeffer_foreman_porteous_loftin_stumpf_werdell_urquhart_albert_darling_2021, title={Assessing cyanobacterial frequency and abundance at surface waters near drinking water intakes across the United States}, volume={201}, ISSN={["1879-2448"]}, DOI={10.1016/j.watres.2021.117377}, abstractNote={This study presents the first large-scale assessment of cyanobacterial frequency and abundance of surface water near drinking water intakes across the United States. Public water systems serve drinking water to nearly 90% of the United States population. Cyanobacteria and their toxins may degrade the quality of finished drinking water and can lead to negative health consequences. Satellite imagery can serve as a cost-effective and consistent monitoring technique for surface cyanobacterial blooms in source waters and can provide drinking water treatment operators information for managing their systems. This study uses satellite imagery from the European Space Agency's Ocean and Land Colour Instrument (OLCI) spanning June 2016 through April 2020. At 300-m spatial resolution, OLCI imagery can be used to monitor cyanobacteria in 685 drinking water sources across 285 lakes in 44 states, referred to here as resolvable drinking water sources. First, a subset of satellite data was compared to a subset of responses (n = 84) submitted as part of the U.S. Environmental Protection Agency's fourth Unregulated Contaminant Monitoring Rule (UCMR 4). These UCMR 4 qualitative responses included visual observations of algal bloom presence and absence near drinking water intakes from March 2018 through November 2019. Overall agreement between satellite imagery and UCMR 4 qualitative responses was 94% with a Kappa coefficient of 0.70. Next, temporal frequency of cyanobacterial blooms at all resolvable drinking water sources was assessed. In 2019, bloom frequency averaged 2% and peaked at 100%, where 100% indicated a bloom was always present at the source waters when satellite imagery was available. Monthly cyanobacterial abundances were used to assess short-term trends across all resolvable drinking water sources and effect size was computed to provide insight on the number of years of data that must be obtained to increase confidence in an observed change. Generally, 2016 through 2020 was an insufficient time period for confidently observing changes at these source waters; on average, a decade of satellite imagery would be required for observed environmental trends to outweigh variability in the data. However, five source waters did demonstrate a sustained short-term trend, with one increasing in cyanobacterial abundance from June 2016 to April 2020 and four decreasing.}, journal={WATER RESEARCH}, author={Coffer, Megan M. and Schaeffer, Blake A. and Foreman, Katherine and Porteous, Alex and Loftin, Keith A. and Stumpf, Richard P. and Werdell, P. Jeremy and Urquhart, Erin and Albert, Ryan J. and Darling, John A.}, year={2021}, month={Aug} }
 @article{coffer_schaeffer_salls_urquhart_loftin_stumpf_werdell_darling_2021, title={Satellite remote sensing to assess cyanobacterial bloom frequency across the United States at multiple spatial scales}, volume={128}, ISSN={["1872-7034"]}, DOI={10.1016/j.ecolind.2021.107822}, abstractNote={Cyanobacterial blooms can have negative effects on human health and local ecosystems. Field monitoring of cyanobacterial blooms can be costly, but satellite remote sensing has shown utility for more efficient spatial and temporal monitoring across the United States. Here, satellite imagery was used to assess the annual frequency of surface cyanobacterial blooms, defined for each satellite pixel as the percentage of images for that pixel throughout the year exhibiting detectable cyanobacteria. Cyanobacterial frequency was assessed across 2,196 large lakes in 46 states across the continental United States (CONUS) using imagery from the European Space Agency’s Ocean and Land Colour Instrument for the years 2017 through 2019. In 2019, across all satellite pixels considered, annual bloom frequency had a median value of 4% and a maximum value of 100%, the latter indicating that for those satellite pixels, a cyanobacterial bloom was detected by the satellite sensor for every satellite image considered. In addition to annual pixel-scale cyanobacterial frequency, results were summarized at the lake- and state-scales by averaging annual pixel-scale results across each lake and state. For 2019, average annual lake-scale frequencies also had a maximum value of 100%, and Oregon and Ohio had the highest average annual state-scale frequencies at 65% and 52%. Pixel-scale frequency results can assist in identifying portions of a lake that are more prone to cyanobacterial blooms, while lake- and state-scale frequency results can assist in the prioritization of sampling resources and mitigation efforts. Satellite imagery is limited by the presence of snow and ice, as imagery collected in these conditions are quality flagged and discarded. Thus, annual bloom frequencies within nine climate regions were investigated to determine whether missing data biased results in climate regions more prone to snow and ice, given that their annual summaries would be weighted toward the summer months when cyanobacterial blooms tend to occur. Results were unbiased by the time period selected in most climate regions, but a large bias was observed for the Northwest Rockies and Plains climate region. Moderate biases were observed for the Ohio Valley and the Southeast climate regions. Finally, a clustering analysis was used to identify areas of high and low cyanobacterial frequency across CONUS based on average annual lake-scale cyanobacterial frequencies for 2019. Several clusters were identified that transcended state, watershed, and eco-regional boundaries. Combined with additional data, results from the clustering analysis may offer insight regarding large-scale drivers of cyanobacterial blooms.}, journal={ECOLOGICAL INDICATORS}, author={Coffer, Megan M. and Schaeffer, Blake A. and Salls, Wilson B. and Urquhart, Erin and Loftin, Keith A. and Stumpf, Richard P. and Werdell, P. Jeremy and Darling, John A.}, year={2021}, month={Sep} }
 @article{coffer_schaeffer_zimmerman_hill_li_islam_whitman_2020, title={Performance across WorldView-2 and RapidEye for reproducible seagrass mapping}, volume={250}, ISSN={["1879-0704"]}, DOI={10.1016/j.rse.2020.112036}, abstractNote={Satellite remote sensing offers an effective remedy to challenges in ground-based and aerial mapping that have previously impeded quantitative assessments of global seagrass extent. Commercial satellite platforms offer fine spatial resolution, an important consideration in patchy seagrass ecosystems. Currently, no consistent protocol exists for image processing of commercial data, limiting reproducibility and comparison across space and time. Additionally, the radiometric performance of commercial satellite sensors has not been assessed against the dark and variable targets characteristic of coastal waters. This study compared data products derived from two commercial satellites: DigitalGlobe's WorldView-2 and Planet's RapidEye. A single scene from each platform was obtained at St. Joseph Bay in Florida, USA, corresponding to a November 2010 field campaign. A reproducible processing regime was developed to transform imagery from basic products, as delivered from each company, into analysis-ready data usable for various scientific applications. Satellite-derived surface reflectances were compared against field measurements. WorldView-2 imagery exhibited high disagreement in the coastal blue and blue spectral bands, chronically overpredicting. RapidEye exhibited better agreement than WorldView-2, but overpredicted slightly across all spectral bands. A deep convolutional neural network was used to classify imagery into deep water, land, submerged sand, seagrass, and intertidal classes. Classification results were compared to seagrass maps derived from photointerpreted aerial imagery. This study offers the first radiometric assessment of WorldView-2 and RapidEye over a coastal system, revealing inherent calibration issues in shorter wavelengths of WorldView-2. Both platforms demonstrated as much as 97% agreement with aerial estimates, despite differing resolutions. Thus, calibration issues in WorldView-2 did not appear to interfere with classification accuracy, but could be problematic if estimating biomass. The image processing routine developed here offers a reproducible workflow for WorldView-2 and RapidEye imagery, which was tested in two additional coastal systems. This approach may become platform independent as more sensors become available.}, journal={REMOTE SENSING OF ENVIRONMENT}, author={Coffer, Megan M. and Schaeffer, Blake A. and Zimmerman, Richard C. and Hill, Victoria and Li, Jiang and Islam, Kazi A. and Whitman, Peter J.}, year={2020}, month={Dec} }
 @article{coffer_schaeffer_darling_urquhart_salls_2020, title={Quantifying national and regional cyanobacterial occurrence in US lakes using satellite remote sensing}, volume={111}, ISSN={["1872-7034"]}, DOI={10.1016/j.ecolind.2019.105976}, abstractNote={Cyanobacterial harmful algal blooms are the most common form of harmful algal blooms in freshwater systems throughout the world. However, in situ sampling of cyanobacteria in inland lakes is limited both spatially and temporally. Satellite data has proven to be an effective tool to monitor cyanobacteria in freshwater lakes across the United States. This study uses data from the European Space Agency Envisat MEdium Resolution Imaging Spectrometer and the Sentinel-3 Ocean and Land Color Instrument to provide a national overview of the percentage of lakes experiencing a cyanobacterial bloom on a weekly basis for 2008–2011, 2017, and 2018. A total of 2321 lakes across the contiguous United States were included in the analysis. We examined four different thresholds to define when a waterbody is classified as experiencing a bloom. Across these four thresholds, we explored variability in bloom percentage with changes in seasonality and lake size. As a validation of algorithm performance, we analyzed the agreement between satellite observations and previously established ecological patterns, although data availability in the wintertime limited these comparisons on a year-round basis. Changes in cyanobacterial bloom percentage at the national scale followed the well-known temporal pattern of freshwater blooms. The percentage of lakes experiencing a bloom increased throughout the year, reached a maximum in fall, and decreased through the winter. Wintertime data, particularly in northern regions, were consistently limited due to snow and ice cover. With the exception of the Southeast and South, regional patterns mimicked patterns found at the national scale. The Southeast and South exhibited an unexpected pattern as cyanobacterial bloom percentage reached a maximum in the winter rather than the summer. Lake Jesup in Florida was used as a case study to validate this observed pattern against field observations of chlorophyll a. Results from this research establish a baseline of annual occurrence of cyanobacterial blooms in inland lakes across the United States. In addition, methods presented in this study can be tailored to fit the specific requirements of an individual system or region.}, journal={ECOLOGICAL INDICATORS}, author={Coffer, Megan M. and Schaeffer, Blake A. and Darling, John A. and Urquhart, Erin A. and Salls, Wilson B.}, year={2020}, month={Apr} }
 @article{schaeffer_kamykowski_mckay_sinclair_milligan_2009, title={LIPID CLASS, CAROTENOID, AND TOXIN DYNAMICS OF KARENIA BREVIS (DINOPHYCEAE) DURING DIEL VERTICAL MIGRATION}, volume={45}, ISSN={["1529-8817"]}, DOI={10.1111/j.1529-8817.2008.00627.x}, abstractNote={The internal lipid, carotenoid, and toxin concentrations of Karenia brevis (C. C. Davis) Gert Hansen and Moestrup are influenced by its ability to use ambient light and nutrients for growth and reproduction. This study investigated changes in K. brevis toxicity, lipid class, and carotenoid concentrations in low‐light, nitrate‐replete (250 μmol quanta · m−2 · s−1, 80 μM NO3); high‐light, nitrate‐replete (960 μmol quanta · m−2 · s−1, 80 μM NO3); and high‐light, nitrate‐reduced (960 μmol quanta · m−2 · s−1, <5 μM NO3) mesocosms. Reverse‐phase HPLC quantified the epoxidation state (EPS) of the xanthophyll‐cycle pigments diadinoxanthin and diatoxanthin, and a Chromarod Iatroscan thin layer chromatography/flame ionization detection (TLC/FID) system quantified changes in lipid class concentrations. EPS did not exceed 0.20 in the low‐light mesocosm, but increased to 0.65 in the high‐light mesocosms. Triacylglycerol and monogalactosyldiacylglycerol (MGDG) were the largest lipid classes consisting of 9.3% to 48.7% and 37.3% to 69.7% of total lipid, respectively. Both lipid classes also experienced the greatest concentration changes in high‐light experiments. K. brevis increased EPS and toxin concentrations while decreasing its lipid concentrations under high light. K. brevis may mobilize its toxins into the surrounding environment by reducing lipid concentrations, such as sterols, limiting competition, or toxins are released because lipids are decreased in high light, reducing any protective mechanism against their own toxins.}, number={1}, journal={JOURNAL OF PHYCOLOGY}, author={Schaeffer, Blake A. and Kamykowski, Daniel and McKay, Laurie and Sinclair, Geoff and Milligan, Edward}, year={2009}, month={Feb}, pages={154–163} }
 @article{sweet_morrison_liu_kamykowski_schaeffer_xie_banks_2009, title={Tropical instability wave interactions within the Galapagos Archipelago}, volume={56}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2009.02.005}, abstractNote={Abstract The effects of tropical instability waves (TIW) within the eastern equatorial Pacific during the boreal fall of 2005 were observed in multiple data sets. The TIW cause oscillations of the sea surface temperature (SST), meridional currents ( V ), and 20 °C isotherm (thermocline). A particularly strong 3-wave packet of ∼15-day period TIW passed through the Galapagos Archipelago in Sep and Oct 2005 and their effects were recorded by moored near-surface sensors. Repeat Argo profiles in the archipelago showed that the large temperature (>5 °C) oscillations that occurred were associated with a vertical adjustment within the water column. Numerical simulations report strong oscillations and upwelling magnitudes of ∼5.0 m d −1 near the Tropical Atmosphere Ocean (TAO) buoy at 0°, 95°W and in the Archipelago at 92°W and 90°W. A significant biological response to the TIW passage was observed within the archipelago. Chlorophyll a measured by the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) increased by >30% above 1998–2007 mean concentrations within the central archipelago. The increases coincide with coldest temperatures and the much larger increases within the archipelago as compared to those of 95°W indicate that TIW induced upwelling over the island platform itself brought more iron-enriched upwelling waters into the euphotic zone.}, number={8}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, author={Sweet, W. V. and Morrison, J. M. and Liu, Y. and Kamykowski, D. and Schaeffer, B. A. and Xie, L. and Banks, S.}, year={2009}, month={Aug}, pages={1217–1229} }
 @article{schaeffer_morrison_kamykowski_feldman_xie_liu_sweet_mcculloch_banks_2008, title={Phytoplankton biomass distribution and identification of productive habitats within the Galapagos Marine Reserve by MODIS, a surface acquisition system, and in-situ measurements}, volume={112}, ISSN={["1879-0704"]}, DOI={10.1016/j.rse.2008.03.005}, abstractNote={The Galapagos Marine Reserve (GMR) is one of the most diverse ecosystems in the world. Phytoplankton are the base of the ecosystem food chain for many higher trophic organisms, so identifying phytoplankton biomass distribution is the first step in understanding the dynamic environment for effective management of the GMR. Moderate Resolution Imaging Spectroradiometer (MODIS) and hyperspectral surface acquisition system derived chlorophyll, in-situ chlorophyll fluorescence, nitrate, salinity, and temperature were collected from March 2005 to the onset of a mild El Niño in November 2006. Islands in the eastern GMR, such as San Cristobal and Espanola, are the first to experience impacts of El Niño and southern migration of the Equatorial Front. Productive habitats were defined as surface waters with salinities > 34, temperatures < 24 °C, and chlorophyll a > 0.4 mg m− 3. Six temporally variable productive habitats identified were: west of Isabela Island, southwest of Floreana Island, south of Santa Cruz, between Santiago and Santa Cruz Islands, and on the eastern side near San Cristobal Island. Model results coupled with surface acquisition system derived chlorophyll indicated productive habitats may also occur for short periods and at a distance from islands such as when the Equatorial Undercurrent (EUC) and South Equatorial Current (SEC) collide over the seamounts north of Isabela Island. All productive habitats were related to topographic upwelling from the EUC into surface waters.}, number={6}, journal={REMOTE SENSING OF ENVIRONMENT}, author={Schaeffer, Blake A. and Morrison, John M. and Kamykowski, Daniel and Feldman, Gene C. and Xie, Lian and Liu, Yanyun and Sweet, William and McCulloch, Anita and Banks, Stuart}, year={2008}, month={Jun}, pages={3044–3054} }
 @article{schaeffer_kamykowski_mckay_sinclair_milligan_2007, title={A comparison of photoresponse among ten different Karenia brevis (Dinophyceae) isolates}, volume={43}, ISSN={["1529-8817"]}, DOI={10.1111/j.1529-8817.2007.00377.x}, abstractNote={Many laboratories have solely used the Wilson isolate to physiologically characterize the harmful algal bloom (HAB) dinoflagellate Karenia brevis (C. C. Davis) G. Hansen et Moestrup. However, analysis of one isolate may lead to misinterpretations when extrapolating measurements to field populations. In this study, pulse‐amplitude‐modulated chlorophyll fluorometer (PAM‐FL) relative electron transport rate (ETR), Fv/Fm, and chl were compared with traditional techniques, such as 14C photosynthesis versus irradiance (P–E) curves, DCMU [3‐(3′,4′‐dichlorophenyl)‐1,1‐dimethyl urea] Fv/Fm, and extracted chl. The DCMU and PAM‐FL values of Fv/Fm (r2 = 0.51) and chl (r2 = 0.58) were in good agreement. There was no correlation between 14C and PAM‐FL α, Pmax, and β parameters because PAM‐FL ETR was only a relative measurement. The PAM‐FL techniques were then used to investigate P–E curves, quantum yield of PSII (Fv/Fm), and chl from 10 K. brevis isolates to determine whether one or all isolates would better represent the species. Comparisons were made with a radial photosynthetron, which allowed for controlled conditions of light and temperature. Isolate α, Pmax, and β varied between 0.097 and 0.204 μmol e− · m−2 · s−1 · (μmol quanta · m−2 · s−1)−1, 80.41 and 241 μmol e− · m−2 · s−1, and 0.005 and 0.160 μmol e− · m−2 · s−1 · (μmol quanta · m−2 · s−1)−1, respectively. Either carbon limitation and/or bacterial negative feedback were implicated as the cause of the P–E parameter variability. Furthermore, these results directly contradicted some literature suggestions that K. brevis is a low‐light‐adapted dinoflagellate. Results showed that K. brevis was more than capable of utilizing and surviving in light conditions that may be present on cloudless days off Florida.}, number={4}, journal={JOURNAL OF PHYCOLOGY}, author={Schaeffer, Blake A. and Kamykowski, Daniel and McKay, Laurie and Sinclair, Geoff and Milligan, Edward J.}, year={2007}, month={Aug}, pages={702–714} }
 @article{sweet_morrison_kamykowski_schaeffer_banks_mcculloch_2007, title={Water mass seasonal variability in the Galapagos archipelago}, volume={54}, ISSN={["1879-0119"]}, DOI={10.1016/j.dsr.2007.09.009}, abstractNote={Three hydrographic surveys were conducted within the Galápagos Archipelago during 2005–2006. The surveys captured the surface properties (<80 m) near the extremes and midpoint of the annual cycle of the mean sea surface temperature (SST) and winds. A cooler SST occurs in boreal summer and fall as the southeast trades strengthen. Current data at 110°W show that this coincides with the Equatorial Undercurrent (EUC) becoming weaker and deeper below a strengthening westward South Equatorial Current (SEC). Opposite conditions are generally found in the spring. Meanwhile, the sea surface salinity (SSS) freshens in late winter/spring when the archipelago receives large rainfalls as the Intertropical Convergence Zone (ITCZ) shifts southward, or in late fall when receiving large influxes from the North Equatorial Countercurrent (NECC). As a result, Tropical Surface Waters (TSW) with salinity (S) <34 fill the archipelago from the late fall through early spring. The SSS becomes saltiest in late spring/early summer as the EUC strengthens, resulting in Equatorial Surface Waters (ESW), S>34, throughout the archipelago. Equatorial Surface Waters are present west of Isabela, where the EUC upwells as it interacts with the Galápagos platform. They also are found east of the archipelago in the cold tongue, which extends westward from South America, and therefore may be advected by the SEC into the archipelago. The upwelling west of Isabela creates a consistently shallow 20 °C isotherm (thermocline), which remains elevated across the archipelago. Linear extrapolation of the thermocline depth along the equator from 110 to 95°W gives a good approximation of the thermocline depth within the archipelago from 92 to 89°W.}, number={12}, journal={DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS}, author={Sweet, W. V. and Morrison, J. M. and Kamykowski, D. and Schaeffer, B. A. and Banks, S. and McCulloch, A.}, year={2007}, month={Dec}, pages={2023–2035} }
 @article{mckay_kamykowski_milligan_schaeffer_sinclair_2006, title={Comparison of swimming speed and photophysiological responses to different external conditions among three Karenia brevis strains}, volume={5}, ISSN={["1878-1470"]}, DOI={10.1016/j.hal.2005.12.001}, abstractNote={Behavior, growth, and production are integral in the life history of Karenia brevis, an autotrophic, dinoflagellate HAB species, and are important variables in modeling blooms in the Gulf of Mexico. This study compares swimming speeds, growth rates, and photosynthetic responses of recent isolates of K. brevis (specifically the Apalachicola – APA, Manasota – MAN, and Jacksonville – JAX strains) over a range of light intensities and temperatures. Strain swimming speeds were similar and remained fairly constant from 17 to 30 °C, but decreased markedly at 13 °C. Photosynthetic responses of the strains to different acclimated temperatures had opposite trends with APA exhibiting higher electron transport rates (ETR) at higher temperatures and MAN exhibiting higher ETR at lower temperatures. In the light experiments, the cells’ internal physiological state (represented by photosynthetic yield, ETR, and neutral lipid reserves) and swimming capabilities were examined in the dark after 6 h incubations in the radial photosynthetron. For all strains, at initial incubation light intensities swimming speed decreased and ETR increased. As incubation light intensities increased, ETR decreased and swimming speed increased. At the highest incubation light intensities, ETR and swimming speed decreased. Neutral lipids followed a pattern similar to ETR, only lipids peaked after ETR at a light intensity that corresponded to the increase in swimming speed. The results suggest that cells may partition energy selectively depending on the needs of the cell. Information was combined to characterize a generalized species response to light and temperature ranges.}, number={6}, journal={HARMFUL ALGAE}, author={McKay, Laurie and Kamykowski, Daniel and Milligan, Ed and Schaeffer, Blake and Sinclair, Geoff}, year={2006}, month={Dec}, pages={623–636} }
 @article{sinclair_kamykowski_milligan_schaeffer_2006, title={Nitrate uptake by Karenia brevis. I. Influences of prior environmental exposure and biochemical state on diel uptake of nitrate}, volume={328}, ISSN={["1616-1599"]}, DOI={10.3354/meps328117}, abstractNote={The ability of a Karenia brevis population to persist in an oligotrophic water column depends on how cell physiology and cell behavior contribute to the acquisition of light and nutrients that often are separated in space. We hypothesized that an aggregation of K. brevis, observed under- going a diel vertical migration (DVM) in the bottom half of a 22 m water column on the West Florida Shelf, used the sediments as a nutrient source. We tested how the physiology of K. brevis contributed to the acquisition of nitrate by evaluating how nitrate uptake changed with prior environmental exposure. The experimental conditions simulated the extremes that cells might endure during DVM when migrating up into an oligotrophic water column versus cells that remained near the sediment- water interface. The first culture, representing cells that attained the maximum apex of their migra- tion away from the sediments, was grown under relatively high light (350 μmol quanta m -2 s -1 ) and reached nitrate-depleted conditions (<0.5 μM NO3 - ) prior to the experiment. The second culture, rep- resenting cells that remained near the sediment-water interface, was grown under relatively low light (60 μmol quanta m -2 s -1 ) and nitrate-replete conditions (~20 μM NO3 - ) prior to the experiment. Cells exposed to nitrate-depleted environments for 12 h prior to the experiment enhanced nocturnal uptake compared to cells continuously exposed to nitrate-replete conditions. Changes in cell physi- ology may contribute to nitrate acquisition after descent from oligotrophic environments to areas with elevated nitrate concentrations.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Sinclair, Geoffrey A. and Kamykowski, Daniel and Milligan, Edward and Schaeffer, Blake}, year={2006}, pages={117–124} }
 @article{sinclair_kamykowski_milligan_schaeffer_2006, title={Nitrate uptake by Karenia brevis. II. Behavior and uptake physiology in a nitrate-depleted mesocosm with a bottom nutrient source}, volume={328}, ISSN={["1616-1599"]}, DOI={10.3354/meps328125}, abstractNote={Karenia brevis may optimize growth by alternately maximizing exposure to light, migrating up into an oligotrophic water column during the day, and to nutrients (nitrate), by migrat- ing down to the sediment-water interface at night. Understanding how cell behavior contributes to the acquisition of light and nutrients that are separated in space is critical to understanding how K. brevis populations persist in oligotrophic environments. In response to previous modeling efforts that parameterized cell physiology and behavior in nitrate-replete conditions, we examined similar cellular characteristics in a stratified 1.5 m deep mesocosm. The upper 2/3 of the mesocosm, encom- passing the surface and middle samples, was nitrate depleted (<0.5 µM NO3 - ) and simulated an oligotrophic water column. The lower 1/3 of the mesocosm contained 10 µM NO3 - corresponding to elevated nutrient levels near the sediment-water interface. We sampled uptake rates at 3 depths during the day at light levels of 350, 125 and 60 µmol quanta m -2 s -1 and again at night in the dark. Nocturnal uptake of nitrate in the mesocosm was significantly less than diurnal uptake. Nocturnal uptake rates in the mesocom were intermediate between cells exposed to prolonged nitrate-depleted and nitrate-replete conditions. Both migration, as indicated by diel aggregation patterns, and cell physiology indicate that descent to regions of higher nutrient concentrations were sufficient to main- tain average growth rates of 0.3 div d -1 . Thus, both the physiology and behavior of K. brevis may sup- port populations near the sediment-water interface, where they may grow undetected in offshore oligotrophic water columns.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Sinclair, Geoffrey A. and Kamykowski, Daniel and Milligan, Edward and Schaeffer, Blake}, year={2006}, pages={125–131} }
 @article{spence_schaeffer_thomas_hathaway_olsen_2005, title={Coastal ocean observing technology transfer to educators}, volume={39}, ISSN={["0025-3324"]}, DOI={10.4031/002533205787465931}, abstractNote={Coastal ocean observing systems provide an opportunity to connect scientific concepts, technology and careers to education. These systems also provide outreach opportunities for researchers to connect beyond their peers to the public. Use of real/near real-time coastal ocean observational
 data has local relevance and can generate excitement for teachers and students about the changes and patterns in the ocean environment. New collaborations, strategies and models must be forged between scientists and educators to meet challenges and provide benefits. Challenges include the
 identification of connections between coastal ocean observing science and precollege science standards and curricula, the design of effective professional development workshops to transfer technology to teachers, the development of Web-based observation data that is accessible to teachers
 and their students, and the construction and testing of model inquiry lessons, which include use of real/near real-time observations data and GIS maps. Benefits include outreach opportunities for researchers, inquiry-driven applications for precollege students and the introduction of coastal
 ocean observing to students with the outcome of a highly trained and diverse work force in ocean sciences for the future. Effective strategies for transfer require new opportunities for engagement between scientists and educators, sharing of credit, evaluations, and solid technical reviews
 of all products to ensure scientific and educational accuracy.}, number={4}, journal={MARINE TECHNOLOGY SOCIETY JOURNAL}, author={Spence, L and Schaeffer, BA and Thomas, C and Hathaway, TK and Olsen, M}, year={2005}, pages={78–82} }